[SciPy-Dev] SciPy 0.11.0 Failures in scipy.test()

Wim R. Cardoen wcardoen@gmail....
Wed Apr 10 10:37:28 CDT 2013


Hello Ralf,

Thanks you for your response.
I compiled BLAS and LAPACK from source. This resolved the problem.
In the coming days I plan to replace BLAS and LAPACK by OpenBLAS to speed
up the code.

Best regards,

Wim




On Wed, Apr 3, 2013 at 10:40 AM, Ralf Gommers <ralf.gommers@gmail.com>wrote:

>
>
>
> On Wed, Apr 3, 2013 at 5:00 PM, Wim R. Cardoen <wcardoen@gmail.com> wrote:
>
>> Hello,
>>
>> This morning I installed numpy 1.7.0 and ran its test suite successfully.
>> After installing scipy 0.11.0 I ran the scipy test suite and obtained a
>> bunch of failures. (see below #2).
>>
>> I compiled the source code on the a RHEL6 box using gfortran (GNU Fortran
>> (GCC) 4.4.6)
>> as well as gcc (gcc (GCC) 4.4.6)
>> I used the OS's blas and lapack library and compiled suitesparse myself.
>> Do you have any idea how can I resolve these failures?
>>
>
> These Arpack routines are an endless source of problems. They're sensitive
> to how BLAS/LAPACK was compiled and to 32/64-bit differences. Here's an
> open ticket with a link to a PR with more discussion:
> http://projects.scipy.org/scipy/ticket/1599
>
> If you don't need the functionality, I'd say ignore it. If you do, you can
> try to find a new BLAS/LAPACK or try to actually understand the issue and
> fix it.
>
> Ralf
>
>
>
>
>> Thanks,
>>
>> Wim
>>
>> #1: Configuration to compile scipy 0.11.0
>>
>> ------------------------------------------------------------------------------------------------------------------------------------
>>  import scipy
>> >>> scipy.show_config()
>> blas_info:
>>     libraries = ['blas', 'lapack']
>>     library_dirs = ['/usr/lib64']
>>     language = f77
>> amd_info:
>>     libraries = ['amd']
>>     library_dirs = ['/uufs/
>> chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/lib']
>>     define_macros = [('SCIPY_AMD_H', None)]
>>     swig_opts = ['-I/uufs/
>> chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
>>     include_dirs = ['/uufs/
>> chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
>> lapack_info:
>>     libraries = ['lapack', 'lapack']
>>     library_dirs = ['/usr/lib64']
>>     language = f77
>> atlas_threads_info:
>>   NOT AVAILABLE
>> blas_opt_info:
>>     libraries = ['blas', 'lapack', 'lapack']
>>     library_dirs = ['/usr/lib64']
>>     language = f77
>>     define_macros = [('NO_ATLAS_INFO', 1)]
>> atlas_blas_threads_info:
>>   NOT AVAILABLE
>> umfpack_info:
>>     libraries = ['umfpack', 'amd']
>>     library_dirs = ['/uufs/
>> chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/lib']
>>     define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)]
>>     swig_opts = ['-I/uufs/
>> chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include', '-I/uufs/
>> chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
>>     include_dirs = ['/uufs/
>> chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
>> lapack_opt_info:
>>     libraries = ['lapack', 'lapack', 'blas', 'lapack', 'lapack']
>>     library_dirs = ['/usr/lib64']
>>     language = f77
>>     define_macros = [('NO_ATLAS_INFO', 1)]
>> atlas_info:
>>   NOT AVAILABLE
>> lapack_mkl_info:
>>   NOT AVAILABLE
>> blas_mkl_info:
>>   NOT AVAILABLE
>> atlas_blas_info:
>>   NOT AVAILABLE
>> mkl_info:
>>   NOT AVAILABLE
>>
>> --------------------------------------------------------------------------------------------------------------------------------------
>>
>>
>> #2: Failures after executing the
>> command
>> import scipy
>> scipy.test()
>>
>> ------------------------------
>>
>> -------------------------------------------------------------------------------------------------------------
>> ======================================================================
>> FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2,
>> 'LM', None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'normal')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
>> line 197, in runTest
>>     self.test(*self.arg)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
>> line 257, in eval_evec
>>     assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 1179, in assert_allclose
>>     verbose=verbose, header=header)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 645, in assert_array_compare
>>     raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=0.00178814, atol=0.000357628
>> error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=csr_matrix,
>> OPpart=None, mode=normal
>> (mismatch 100.0%)
>>  x: array([[  2.38156418e-01,  -6.75444982e+09],
>>        [ -1.07853470e-01,  -8.01245676e+09],
>>        [  1.24683023e-01,  -5.19757686e+09],...
>>  y: array([[  2.38156418e-01,  -5.70949789e+08],
>>        [ -1.07853470e-01,  -4.05829392e+08],
>>        [  1.24683023e-01,   6.25800146e+07],...
>>
>> ======================================================================
>> FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2,
>> 'LM', None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'buckling')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
>> line 197, in runTest
>>     self.test(*self.arg)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
>> line 257, in eval_evec
>>     assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 1179, in assert_allclose
>>     verbose=verbose, header=header)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 645, in assert_array_compare
>>     raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=0.00178814, atol=0.000357628
>> error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=csr_matrix,
>> OPpart=None, mode=buckling
>> (mismatch 100.0%)
>>  x: array([[  3.53755447e-01,  -2.29114355e+04],
>>        [ -1.60204595e-01,  -6.65625445e+04],
>>        [  1.85203065e-01,  -2.69012500e+04],...
>>  y: array([[  3.53755447e-01,  -8.88255444e+05],
>>        [ -1.60204595e-01,  -2.39343354e+06],
>>        [  1.85203065e-01,  -3.96842525e+04],...
>>
>> ======================================================================
>> FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2,
>> 'LM', None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'cayley')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
>> line 197, in runTest
>>     self.test(*self.arg)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
>> line 257, in eval_evec
>>     assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 1179, in assert_allclose
>>     verbose=verbose, header=header)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 645, in assert_array_compare
>>     raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=0.00178814, atol=0.000357628
>> error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=csr_matrix,
>> OPpart=None, mode=cayley
>> (mismatch 100.0%)
>>  x: array([[ -2.38156418e-01,   1.04661597e+09],
>>        [  1.07853470e-01,   1.39930271e+09],
>>        [ -1.24683023e-01,   9.56906461e+08],...
>>  y: array([[ -2.38156418e-01,   7.63721281e+07],
>>        [  1.07853470e-01,   1.25169905e+08],
>>        [ -1.24683023e-01,   2.91283130e+07],...
>>
>> ======================================================================
>> FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2,
>> 'LM', None, 0.5, <function asarray at 0xd19a28>, None, 'normal')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
>> line 197, in runTest
>>     self.test(*self.arg)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
>> line 257, in eval_evec
>>     assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 1179, in assert_allclose
>>     verbose=verbose, header=header)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 645, in assert_array_compare
>>     raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=0.000357628, atol=0.000357628
>> error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=asarray,
>> OPpart=None, mode=normal
>> (mismatch 100.0%)
>>  x: array([[ -2.38157020e-01,  -9.38079485e+09],
>>        [  1.07853829e-01,  -1.09927593e+10],
>>        [ -1.24683096e-01,  -7.26035649e+09],...
>>  y: array([[ -2.38157028e-01,  -1.14406333e+09],
>>        [  1.07853849e-01,  -1.61444148e+09],
>>        [ -1.24683097e-01,  -9.66750843e+08],...
>>
>> ======================================================================
>> FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2,
>> 'LM', None, 0.5, <function asarray at 0xd19a28>, None, 'buckling')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
>> line 197, in runTest
>>     self.test(*self.arg)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
>> line 257, in eval_evec
>>     assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 1179, in assert_allclose
>>     verbose=verbose, header=header)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 645, in assert_array_compare
>>     raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=0.000357628, atol=0.000357628
>> error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=asarray,
>> OPpart=None, mode=buckling
>> (mismatch 100.0%)
>>  x: array([[  3.53756177e-01,   3.54742236e+05],
>>        [ -1.60205036e-01,   9.37802669e+05],
>>        [  1.85203150e-01,  -6.91305082e+04],...
>>  y: array([[  3.53756197e-01,   1.19154973e+07],
>>        [ -1.60205063e-01,   3.16087279e+07],
>>        [  1.85203158e-01,  -2.15500940e+06],...
>>
>> ======================================================================
>> FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2,
>> 'LM', None, 0.5, <function asarray at 0xd19a28>, None, 'cayley')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
>> line 197, in runTest
>>     self.test(*self.arg)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
>> line 257, in eval_evec
>>     assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 1179, in assert_allclose
>>     verbose=verbose, header=header)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 645, in assert_array_compare
>>     raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=0.000357628, atol=0.000357628
>> error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=asarray,
>> OPpart=None, mode=cayley
>> (mismatch 100.0%)
>>  x: array([[ -2.38156244e-01,   3.27365597e+08],
>>        [  1.07853608e-01,   4.31395993e+08],
>>        [ -1.24682902e-01,   2.93518385e+08],...
>>  y: array([[ -2.38156393e-01,   2.20001033e+07],
>>        [  1.07853475e-01,   3.05206768e+07],
>>        [ -1.24683015e-01,   8.50334431e+06],...
>> ======================================================================
>> FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2,
>> 'SM', None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'buckling')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
>> line 197, in runTest
>>     self.test(*self.arg)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
>> line 257, in eval_evec
>>     assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 1179, in assert_allclose
>>     verbose=verbose, header=header)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 645, in assert_array_compare
>>     raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=0.00178814, atol=0.000357628
>> error for eigsh:standard, typ=f, which=SM, sigma=0.5, mattype=csr_matrix,
>> OPpart=None, mode=buckling
>> (mismatch 100.0%)
>>  x: array([[  3.32810915e-02,  -1.39781114e+06],
>>        [  8.83144107e-02,   6.75649002e+05],
>>        [ -5.86642416e-03,  -6.19039713e+05],...
>>  y: array([[  3.32810915e-02,  -2.24275052e+05],
>>        [  8.83144107e-02,   1.08299209e+05],
>>        [ -5.86642416e-03,  -9.86191556e+04],...
>>
>> ======================================================================
>> FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2,
>> 'SM', None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'cayley')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
>> line 197, in runTest
>>     self.test(*self.arg)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
>> line 257, in eval_evec
>>     assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 1179, in assert_allclose
>>     verbose=verbose, header=header)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 645, in assert_array_compare
>>     raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=0.00178814, atol=0.000357628
>> error for eigsh:standard, typ=f, which=SM, sigma=0.5, mattype=csr_matrix,
>> OPpart=None, mode=cayley
>> (mismatch 100.0%)
>>  x: array([[  3.87506792e-03,   4.25513135e+07],
>>        [  1.02828460e-02,  -1.78393819e+07],
>>        [ -6.83054282e-04,  -3.54143274e+07],...
>>  y: array([[  3.87506792e-03,   2.90700178e+08],
>>        [  1.02828460e-02,  -1.18728352e+08],
>>        [ -6.83054282e-04,  -2.87462041e+08],...
>>
>> ======================================================================
>> .......
>>
>>
>> ======================================================================
>> FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'd', 2,
>> 'SA', None, 0.5, <function asarray at 0xd19a28>, None, 'cayley')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
>> line 197, in runTest
>>     self.test(*self.arg)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
>> line 257, in eval_evec
>>     assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 1179, in assert_allclose
>>     verbose=verbose, header=header)
>>   File "/uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
>> line 645, in assert_array_compare
>>     raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=4.44089e-13, atol=4.44089e-13
>> error for eigsh:general, typ=d, which=SA, sigma=0.5, mattype=asarray,
>> OPpart=None, mode=cayley
>> (mismatch 100.0%)
>>  x: array([[-0.36892684, -0.01935691],
>>        [-0.26850996, -0.11053158],
>>        [-0.40976156, -0.13223572],...
>>  y: array([[-0.43633077, -0.01935691],
>>        [-0.25161386, -0.11053158],
>>        [-0.36756684, -0.13223572],...
>>
>> ----------------------------------------------------------------------
>> Ran 5481 tests in 75.399s
>>
>> FAILED (KNOWNFAIL=15, SKIP=41, failures=63)
>> Running unit tests for scipy
>> NumPy version 1.7.0
>> NumPy is installed in /uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy
>> SciPy version 0.11.0
>> SciPy is installed in /uufs/
>> chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy
>> Python version 2.7.3 (default, Mar 28 2013, 15:20:19) [GCC 4.4.6 20120305
>> (Red Hat 4.4.6-4)]
>> nose version 1.1.2
>>
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev@scipy.org
>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>
>>
>
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